@article{ohata_2024, title={Friedel-Crafts Reactions for Biomolecular Chemistry}, url={https://doi.org/10.26434/chemrxiv-2024-rd9wn}, DOI={10.26434/chemrxiv-2024-rd9wn}, abstractNote={Chemical tools and principles have become central to biological and medical research/applications by leveraging a range of classical organic chemistry reactions. Friedel-Crafts alkylation and acylation are arguably one of the most well-known and used synthetic methods for preparation of small molecules but its use in biological and medical fields are relatively less frequent than the other reactions, possibly owing to the notion about its plausible incompatibility with biological systems. This Review demonstrates advances of Friedel-Crafts alkylation and acylation reactions in a variety of biomolecular chemistry fields. With the discoveries and applications of numerous biomolecule-catalyzed or –assisted processes, the reactions have garnered considerable interests in biochemistry, enzymology, and biocatalysis. Despite the challenges of reactivity and selectivity of biomolecular reactions, the alkylation and acylation reactions demonstrated its utility for construction and functionalization of all the four major biomolecules (i.e., nucleosides, carbohydrates/saccharides, lipids/fatty acids, and amino acids/peptides/proteins), and their diverse applications in biological, medical, and material fields are discussed. As the alkylation and acylation reactions are often fundamental educational components of organic chemistry courses, the Review is intended for both experts and nonexperts by discussing their basic reaction patterns (with the depiction of each reaction mechanism in the Electronic Supplementary Information) and relevant real-world impacts in order to enrich chemical research and education. The significant growth of biomolecular Friedel-Crafts reactions described here is a testament to its broad importance and utility, and the further development and investigation of the reactions will surely be the focus in the organic biomolecular chemistry fields.}, author={Ohata, Jun}, year={2024}, month={Mar} }
 @article{nuruzzaman_colella_uzoewulu_meo_gross_ishizawa_sana_zhang_hoff_medlock_et al._2024, title={Hexafluoroisopropanol as a Bioconjugation Medium of Ultrafast, Tryptophan-Selective Catalysis}, volume={2}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.3c13447}, abstractNote={The past decade has seen a remarkable growth in the number of bioconjugation techniques in chemistry, biology, material science, and biomedical fields. A core design element in bioconjugation technology is a chemical reaction that can form a covalent bond between the protein of interest and the labeling reagent. Achieving chemoselective protein bioconjugation in aqueous media is challenging, especially for generally less reactive amino acid residues, such as tryptophan. We present here the development of tryptophan-selective bioconjugation methods through ultrafast Lewis acid-catalyzed reactions in hexafluoroisopropanol (HFIP). Structure-reactivity relationship studies have revealed a combination of thiophene and ethanol moieties to give a suitable labeling reagent for this bioconjugation process, which enables modification of peptides and proteins in an extremely rapid reaction unencumbered by noticeable side reactions. The capability of the labeling method also facilitated radiofluorination application as well as antibody functionalization. Enhancement of an α-helix by HFIP leads to its compatibility with a certain protein, and this report also demonstrates a further stabilization strategy achieved by the addition of an ionic liquid to the HFIP medium. The nonaqueous bioconjugation approaches allow access to numerous chemical reactions that are unavailable in traditional aqueous processes and will further advance the chemistry of proteins.}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Nuruzzaman, Mohammad and Colella, Brandon M. and Uzoewulu, Chiamaka P. and Meo, Alissa E. and Gross, Elizabeth J. and Ishizawa, Seiya and Sana, Sravani and Zhang, He and Hoff, Meredith E. and Medlock, Bryce T. W. and et al.}, year={2024}, month={Feb} }
 @article{ohata_2023, title={Chemical labeling strategies using biomolecule-compatible, nonaqueous media}, url={https://doi.org/10.48321/D1536T}, DOI={10.48321/D1536T}, author={Ohata, Jun}, year={2023}, month={Sep} }
 @article{nizam_stowe_mckinney_ohata_2023, title={Iron-sensitive protein conjugates formed with a Wittig reaction precursor in ionic liquid}, volume={59}, ISSN={["1364-548X"]}, url={https://doi.org/10.1039/D3CC03825D}, DOI={10.1039/D3CC03825D}, abstractNote={In this report, formation of protein conjugates with an iron-sensitive enamine linkage is demonstrated through the ionic liquid-based bioconjugation method.}, number={81}, journal={CHEMICAL COMMUNICATIONS}, author={Nizam, Zeinab M. and Stowe, Ashton M. and Mckinney, Jada K. and Ohata, Jun}, year={2023}, month={Oct}, pages={12160–12163} }
 @article{nizam_stowe_mckinney_ohata_2023, title={Iron-sensitive protein conjugates formed with a Wittig reaction precursor in ionic liquid}, volume={9}, ISSN={["1364-548X"]}, DOI={10.1039/d3cc03825}, journal={CHEMICAL COMMUNICATIONS}, author={Nizam, Zeinab M. and Stowe, Ashton M. and Mckinney, Jada K. and Ohata, Jun}, year={2023}, month={Sep} }
 @article{colella_ohata_2023, title={Small-Molecule CO<sub>2</sub> Donors Accelerate Three-Component Peptide/Protein Bioconjugation with Alkylazides and Phosphines in Ionic Liquids}, volume={12}, ISSN={["1437-2096"]}, url={https://doi.org/10.1055/a-2212-7816}, DOI={10.1055/a-2212-7816}, abstractNote={Development of chemical modification techniques for peptides and proteins has been facilitated by a set of multicomponent reactions to date. This Letter demonstrates use of small molecule CO2 donors to promote reaction efficiency of the coupling of alkylamine on peptides and proteins with azide-derived iminophosphorane and carbon dioxide.}, journal={SYNLETT}, author={Colella, Brandon M. and Ohata, Jun}, year={2023}, month={Dec} }
 @article{hoshi_messina_ohata_chung_chang_2022, title={A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues}, volume={5}, ISSN={["1750-2799"]}, url={https://doi.org/10.1038/s41596-022-00694-7}, DOI={10.1038/s41596-022-00694-7}, abstractNote={Hydrogen peroxide (H2O2) is a key member of the reactive oxygen species family of transient small molecules that has broad contributions to oxidative stress and redox signaling. The development of selective and sensitive chemical probes can enable the study of H2O2 biology in cell, tissue and animal models. Peroxymycin-1 is a histochemical activity-based sensing probe that responds to H2O2 via chemoselective boronate oxidation to release puromycin, which is then covalently incorporated into nascent proteins by the ribosome and can be detected by antibody staining. Here, we describe an optimized two-step, one-pot protocol for synthesizing Peroxymycin-1 with improved yields over our originally reported procedure. We also present detailed procedures for applying Peroxymycin-1 to a broad range of biological samples spanning cells to animal tissues for profiling H2O2 levels through histochemical detection by using commercially available anti-puromycin antibodies. The preparation of Peroxymycin-1 takes 9 h, the confocal imaging experiments of endogenous H2O2 levels across different cancer cell lines take 1 d, the dot blot analysis of mouse liver tissues takes 1 d and the confocal imaging of mouse liver tissues takes 3-4 d.}, journal={NATURE PROTOCOLS}, author={Hoshi, Kaede and Messina, Marco S. and Ohata, Jun and Chung, Clive Yik-Sham and Chang, Christopher J.}, year={2022}, month={May} }
 @article{el-shaffey_gross_hall_ohata_2022, title={Correction to “An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine–Azide Bioconjugation Method”}, volume={5}, url={https://doi.org/10.1021/jacs.2c04141}, DOI={10.1021/jacs.2c04141}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to “An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine–Azide Bioconjugation Method”Hisham M. El-ShaffeyHisham M. El-ShaffeyMore by Hisham M. El-Shaffeyhttps://orcid.org/0000-0003-4117-1378, Elizabeth J. GrossElizabeth J. GrossMore by Elizabeth J. Grosshttps://orcid.org/0000-0003-2153-5381, Yvonne D. HallYvonne D. HallMore by Yvonne D. Hallhttps://orcid.org/0000-0001-9405-4867, and Jun Ohata*Jun OhataMore by Jun Ohatahttps://orcid.org/0000-0002-3614-7472Cite this: J. Am. Chem. Soc. 2022, 144, 20, 9178–9180Publication Date (Web):May 14, 2022Publication History Published online14 May 2022Published inissue 25 May 2022https://doi.org/10.1021/jacs.2c04141Copyright © 2022 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2591Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={El-Shaffey, Hisham M. and Gross, Elizabeth J. and Hall, Yvonne D. and Ohata, Jun}, year={2022}, month={May} }
 @article{ohata_hall_uzoewulu_nizam_ishizawa_el-shaffey_2022, title={Phosphine-Mediated Three-Component Bioconjugation of Amino- and Azidosaccharides in Ionic Liquids}, volume={4}, url={https://doi.org/10.26434/chemrxiv-2022-k76gn}, DOI={10.26434/chemrxiv-2022-k76gn}, abstractNote={Bioconjugation of carbohydrates has advanced the modern chemical biology and medical science research by incorporation of desired functionalities to the oxygen-rich biomolecules. However, the labeling process or selective chemical reaction of carbohydrates have been a challenging task because of their chemical, functional, and structural diversities, and no single chemical modification tool can be universally applicable to all the target substrates in different environments. In this report, we have developed a bioconjugation strategy for labeling of carbohydrate derivatives through a phosphine-mediated three-component coupling reaction in an ionic liquid medium. The multiple characterization methods identified a urea group as the reaction product of the phosphine-mediated coupling through the installation of carbonyl group from carbon dioxide in air and loss of nitrogen gas from the azide group. We have developed purification protocols to facilitate the cleanup and analysis of ionic liquid-based bioconjugation processes, which can be used for a diverse set of carbohydrate derivatives. The phosphine-mediated urea-forming reaction was applied to a variety of amine- and azide-containing carbohydrates such as antibiotics, anti-tumor agent, and polysaccharide with corresponding azide- and amine-based reagent, respectively. The ionic liquid-based bioconjugation was amenable for the chemical modification of the mammalian cell lysate in an azide-dependent manner. Thus, the present report represents not only the advancement of the nonaqueous bioconjugation method for carbohydrate derivatives from the reaction development perspectives, but also their practical utility for creation of carbohydrate conjugates as well as a study tool of the biomolecule through the bioorthogonal chemistry-like reactivity.}, publisher={American Chemical Society (ACS)}, author={Ohata, Jun and Hall, Yvonne and Uzoewulu, Chiamaka and Nizam, Zeinab and Ishizawa, Seiya and El-Shaffey, Hisham}, year={2022}, month={Apr} }
 @article{hall_uzoewulu_nizam_ishizawa_el-shaffey_ohata_2022, title={Phosphine-mediated three-component bioconjugation of amino- and azidosaccharides in ionic liquids}, volume={8}, ISSN={["1364-548X"]}, url={https://doi.org/10.1039/D2CC04013A}, DOI={10.1039/D2CC04013A}, abstractNote={Bioconjugation of carbohydrates has been a challenging task because of their chemical, functional, and structural diversities, and no single chemical modification tool can be universally applicable to all the target substrates in different environments. In this report, we have developed a bioconjugation strategy for labeling of carbohydrate derivatives through a phosphine-mediated three-component coupling reaction in an ionic liquid medium.}, journal={CHEMICAL COMMUNICATIONS}, publisher={Royal Society of Chemistry (RSC)}, author={Hall, Yvonne D. and Uzoewulu, Chiamaka P. and Nizam, Zeinab M. and Ishizawa, Seiya and El-Shaffey, Hisham M. and Ohata, Jun}, year={2022}, month={Aug} }
 @article{ishizawa_tumurkhuu_gross_ohata_2022, title={Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids}, volume={1}, ISSN={["2041-6539"]}, url={https://doi.org/10.1039/D1SC05204G}, DOI={10.1039/D1SC05204G}, abstractNote={Development of multiple chemical tools for deoxyribonucleic acid (DNA) labeling has facilitated wide use of their functionalized conjugates, but significant practical and methodological challenges remain to achievement of site-specific chemical modification of the biomacromolecule. As covalent labeling processes are more challenging in aqueous solution, use of nonaqueous, biomolecule-compatible solvents such as an ionic liquid consisting of a salt with organic molecule architecture, could be remarkably helpful in this connection. Herein, we demonstrate site-specific chemical modification of unprotected DNAs through a tetrazene-forming amine–azide coupling reaction using an ionic liquid. This ionic liquid-enhanced reaction process has good functional group tolerance and precise chemoselectivity, and enables incorporation of various useful functionalities such as biotin, cholesterol, and fluorophores. A site-specifically labeled oligonucleotide, or aptamer interacting with a growth factor receptor (Her2) was successfully used in the fluorescence imaging of breast cancer cell lines. The non-traditional medium-promoted labeling strategy described here provides an alternative design paradigm for future development of chemical tools for applications involving DNA functionalization.}, journal={CHEMICAL SCIENCE}, publisher={Royal Society of Chemistry (RSC)}, author={Ishizawa, Seiya and Tumurkhuu, Munkhtuya and Gross, Elizabeth J. and Ohata, Jun}, year={2022}, month={Jan} }
 @article{ishizawa_tumurkhuu_gross_ohata_2022, title={Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids (vol 13, pg 1780, 2022)}, volume={13}, ISSN={["2041-6539"]}, DOI={10.1039/d2sc90102a}, abstractNote={Correction for ‘Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids’ by Seiya Ishizawa et al., Chem. Sci., 2022, 13, 1780–1788, https://doi.org/10.1039/d1sc05204g.}, number={22}, journal={CHEMICAL SCIENCE}, author={Ishizawa, Seiya and Tumurkhuu, Munkhtuya and Gross, Elizabeth J. and Ohata, Jun}, year={2022}, month={Jun}, pages={6749–6751} }
 @article{uzoewulu_ohata_2022, title={Translation of a Phosphine- and Azide-Based Reaction to Chemical Modification of Biomolecules in Ionic Liquid}, volume={7}, ISSN={["1437-2096"]}, url={https://doi.org/10.1055/a-1908-2066}, DOI={10.1055/a-1908-2066}, abstractNote={The difference of reaction design principles between traditional, small molecule synthetic chemistry and biomolecular chemical reactions prevented the simple translation of small molecule chemistry into biomolecular reactions. One of the key challenges of bioconjugation, or reactions on biomolecules, are the necessity of aqueous solutions as the solvent. In this Synpact article, we describe our pursuit of using an ionic liquid as a nonaqueous reaction medium to conduct phosphine- and azide-based bioconjugation reactions.}, journal={SYNLETT}, publisher={Georg Thieme Verlag KG}, author={Uzoewulu, Chiamaka P. and Ohata, Jun}, year={2022}, month={Aug} }
 @article{uzoewulu_ohata_2022, title={Translation of a phosphine- and azide-based reaction to chemical modification of biomolecules in ionic liquid}, url={https://doi.org/10.26434/chemrxiv-2022-k3rc1}, DOI={10.26434/chemrxiv-2022-k3rc1}, abstractNote={The difference of reaction design principles between traditional, small molecule synthetic chemistry and biomolecular chemical reactions prevented the simple translation of small molecule chemistry into biomolecular reactions. One of the key challenges of bioconjugation, or reactions on biomolecules, are the necessity of aqueous solutions as the solvent. In this Synpact article, we describe our pursuit of using an ionic liquid as a nonaqueous reaction medium to conduct phosphine- and azide-based bioconjugation reactions.}, author={Uzoewulu, Chiamaka and Ohata, Jun}, year={2022}, month={Jul} }
 @article{el-shaffey_gross_hall_ohata_2021, title={An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine-Azide Bioconjugation Method}, volume={143}, ISSN={["1520-5126"]}, url={https://doi.org/10.1021/jacs.1c06092}, DOI={10.1021/jacs.1c06092}, abstractNote={While a diverse set of design strategies have produced various chemical tools for biomolecule labeling in aqueous media, the development of nonaqueous, biomolecule-compatible media for bioconjugation has significantly lagged behind. In this report, we demonstrate that an aprotic ionic liquid serves as a novel reaction solvent for protein bioconjugation without noticeable loss of the biomolecule functions. The ionic liquid bioconjugation approach led to discovery of a novel triphenylphosphine-mediated amine-azide coupling reaction that forges a stable tetrazene linkage on unprotected peptides and proteins. This strategy of using untraditional media would provide untapped opportunities for expanding the scope of chemical approaches for bioconjugation.}, number={33}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, publisher={American Chemical Society (ACS)}, author={El-Shaffey, Hisham M. and Gross, Elizabeth J. and Hall, Yvonne D. and Ohata, Jun}, year={2021}, month={Aug}, pages={12974–12979} }
 @article{ohata_teramoto_fujita_takemoto_matsuzaka_2021, title={Linear Hydrocarbon Chain Growth from a Molecular Diruthenium Carbide Platform}, volume={143}, ISSN={["1520-5126"]}, url={https://doi.org/10.1021/jacs.1c06586}, DOI={10.1021/jacs.1c06586}, abstractNote={The formation of linear hydrocarbon chains by sequential coupling of C1 units on the metal surface is the central part of the Fischer-Tropsch (F-T) synthesis. Organometallic complexes have provided numerous models of relevant individual C-C coupling events but have failed to reproduce the complete chain lengthening sequence that transforms a linear Cn hydrocarbon chain into its Cn+1 homologue in an iterative fashion. In this work, we demonstrate stepwise growth of linear Cn hydrocarbon chains and their conversion to their Cn+1 homologues via consecutive addition of CH2 units on a molecular diruthenium carbide platform. The chain growth sequence is initiated by the formation of a μ-η1:η1-C═CH2 ligand from a C + CH2 coupling between the μ-carbido complex [(Cp*Ru)2(η-NPh)(μ-C)] (1; Cp* = η5-C5Me5) and Ph2SCH2. Then, the chain propagates via a general C═CHR + CH2 coupling and subsequent hydrogen-assisted isomerization of the resulting allene ligand μ-η1:η3-H2C═C═CHR to a higher vinylidene homologue μ-η1:η1-C═CH(CH2)R. By repeating this reaction sequence, up to C6 chains have been synthesized in a stepwise fashion. The key step of this chain homologation sequence is the selective hydrogenation of the μ-η1:η3-allene unit to the corresponding μ-alkylidene ligand. Isotope labeling and computational studies indicate that this transformation proceeds via the hydrogenation of the allene ligand to a terminal alkene form and its isomerization to the μ-alkylidene ligand facilitated by the coordinatively unsaturated diruthenium platform.}, number={39}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, publisher={American Chemical Society (ACS)}, author={Ohata, Jun and Teramoto, Akira and Fujita, Hiroaki and Takemoto, Shin and Matsuzaka, Hiroyuki}, year={2021}, month={Oct}, pages={16105–16112} }
 @article{ishizawa_tumurkhuu_gross_ohata_2021, title={Site-Specific DNA Functionalization through the Tetrazene-Forming Reaction in Ionic Liquids}, volume={9}, url={https://doi.org/10.33774/chemrxiv-2021-zkz9w}, DOI={10.33774/chemrxiv-2021-zkz9w}, abstractNote={Development of multiple chemical tools for deoxynucleic acid (DNA) labeling has facilitated wide use of their functionalized conjugates, but significant practical and methodological challenges remain to achievement of site-specific chemical modification of the biomacromolecule. As covalent labeling processes are more challenging in aqueous solution, use of nonaqueous, biomolecule-compatible solvents such as an ionic liquid consisting of a salt with organic molecule architecture, could be remarkably helpful in this connection. Herein, we demonstrate site-specific chemical modification of DNAs through a tetrazene-forming amine-azide coupling reaction using an ionic liquid. This ionic liquid-enhanced reaction process has good functional group tolerance and precise chemoselectivity, and enables incorporation into DNA of various useful functionalities such as biotin, cholesterol and fluorophores which could be incorporated into DNA through this method. A site-specifically labeled single stranded nucleotide, or aptamer interacting with a growth factor receptor (Her2) was successfully used in the fluorescence imaging of breast cancer cell lines. The non-traditional medium-promoted labeling strategy described here provides an alternative design paradigm for future development of chemical tools for applications involving DNA functionalization.}, publisher={Cambridge University Press (CUP)}, author={Ishizawa, Seiya and Tumurkhuu, Munkhtuya and Gross, Elizabeth and Ohata, Jun}, year={2021}, month={Sep} }
 @article{ishizawa_tumurkhuu_gross_ohata_2021, title={Site-Specific DNA Functionalization through the Tetrazene-Forming Reaction in Ionic Liquids}, volume={9}, url={https://doi.org/10.26434/chemrxiv-2021-zkz9w}, DOI={10.26434/chemrxiv-2021-zkz9w}, abstractNote={Development of multiple chemical tools for deoxynucleic acid (DNA) labeling has facilitated wide use of their functionalized conjugates, but significant practical and methodological challenges remain to achievement of site-specific chemical modification of the biomacromolecule. As covalent labeling processes are more challenging in aqueous solution, use of nonaqueous, biomolecule-compatible solvents such as an ionic liquid consisting of a salt with organic molecule architecture, could be remarkably helpful in this connection. Herein, we demonstrate site-specific chemical modification of DNAs through a tetrazene-forming amine-azide coupling reaction using an ionic liquid. This ionic liquid-enhanced reaction process has good functional group tolerance and precise chemoselectivity, and enables incorporation into DNA of various useful functionalities such as biotin, cholesterol and fluorophores which could be incorporated into DNA through this method. A site-specifically labeled single stranded nucleotide, or aptamer interacting with a growth factor receptor (Her2) was successfully used in the fluorescence imaging of breast cancer cell lines. The non-traditional medium-promoted labeling strategy described here provides an alternative design paradigm for future development of chemical tools for applications involving DNA functionalization.}, publisher={American Chemical Society (ACS)}, author={Ishizawa, Seiya and Tumurkhuu, Munkhtuya and Gross, Elizabeth and Ohata, Jun}, year={2021}, month={Sep} }
 @article{ohata_krishnamoorthy_gonzalez_xiao_iovan_toste_miller_chang_2020, title={An Activity-Based Methionine Bioconjugation Approach To Developing Proximity-Activated Imaging Reporters}, volume={6}, url={https://doi.org/10.1021/acscentsci.9b01038}, DOI={10.1021/acscentsci.9b01038}, abstractNote={Chemical probes that report on protein activity, rather than protein abundance, with spatial and temporal resolution can enable studies of their native function in biological contexts as well as provide opportunities for developing new types of biochemical reporters. Here we present a sensing platform, termed proximity-activated imaging reporter (PAIR), which combines activity-based methionine bioconjugation and antibody labeling with proximity-dependent oligonucleotide-based amplification to monitor dynamic changes of a given analyte in cells and animals through context-dependent methionine labeling of specific protein targets. We establish this PAIR method to develop sensors for imaging reactive oxygen species (ROS) and calcium ions through oxaziridine-directed labeling of reactive methionine residues on β-actin and calmodulin (CaM), respectively, where the extent of methionine bioconjugation on these protein targets can serve as an indicator of oxidative stress or calcium status. In particular, application of PAIR to activity-based CaM detection provides a method for imaging integrated calcium activity in both in vitro cell and in vivo zebrafish models. By relying on native protein biochemistry, PAIR enables redox and metal imaging without introduction of external small molecules or genetically encoded indicators that can potentially buffer the natural/existing pools. This approach can be potentially generalized to target a broader range of analytes by pairing appropriate activity-based protein probes with protein detection reagents in a proximity-driven manner, providing a starting point not only for designing new sensors but also for monitoring endogenous activity of specific protein targets in biological specimens with spatial and temporal fidelity.}, number={1}, journal={ACS Central Science}, publisher={American Chemical Society (ACS)}, author={Ohata, Jun and Krishnamoorthy, Lakshmi and Gonzalez, Monica A. and Xiao, Tong and Iovan, Diana A. and Toste, F. Dean and Miller, Evan W. and Chang, Christopher J.}, year={2020}, month={Jan}, pages={32–40} }
 @article{activity-based sensing methods for monitoring the reactive carbon species carbon monoxide and formaldehyde in living systems_2019, url={http://dx.doi.org/10.1021/acs.accounts.9b00386}, DOI={10.1021/acs.accounts.9b00386}, abstractNote={Carbon is central to the chemistry of life, and in addition to its fundamental roles as a static component of all major biomolecules spanning proteins, nucleic acids, sugars, and lipids, emerging evidence shows that small and transient carbon-based metabolites, termed reactive carbon species (RCS), are dynamic signaling/stress agents that can influence a variety of biological pathways. Recent examples include the identification of carbon monoxide (CO) as an ion channel blocker and endogenous formaldehyde (FA) as a one-carbon metabolic unit formed from the spontaneous degradation of dietary folate metabolites. These findings motivate the development of analytical tools for transient carbon species that can achieve high specificity and sensitivity to further investigate RCS signaling and stress pathways at the cell, tissue, and whole-organism levels. This Account summarizes work from our laboratory on the development of new chemical tools to monitor two important one-carbon RCS, CO and FA, through activity-based sensing (ABS), where we leverage the unique chemical reactivities of these small and transient analytes, rather than lock-and-key binding considerations, for selective detection. Classic inorganic/organometallic and organic transformations form the basis for this approach. For example, to distinguish CO from other biological diatomics of similar shape and size (e.g., nitric oxide and oxygen), we exploit palladium-mediated carbonylation as a synthetic method for CO sensing. The high selectivity of this carbonylation approach successfully enables imaging of dynamic changes in intracellular CO levels in live cells. Likewise, we apply the aza-Cope reaction for FA detection to provide high selectivity for this one-carbon unit over other larger biological aldehydes that are reactive electrophiles, such as acetaldehyde and methylglyoxal. By relying on an activity-based trigger as a design principle for small-molecule detection, this approach can be generalized to create a toolbox of selective FA imaging reagents, as illustrated by a broad range of FA probes spanning turn-on and ratiometric fluorescence imaging, positron emission tomography imaging, and chemiluminescence imaging modalities. Moreover, these chemical tools have revealed new one-carbon biology through the identification of folate as a dietary source of FA and alcohol dehydrogenase 5 as a target for FA metabolism. Indeed, these selective RCS detection methods have been expanded to a wider array of imaging platforms, such as metal-complex-based time-gated luminescence and materials-based imaging scaffolds (e.g., nanotubes, nanoparticles, and carbon dots), with modalities extending to Raman and Rayleigh scattering readouts. This pursuit of leveraging selective chemical reactivity to develop highly specific ABS probes for imaging of RCS provides not only practical tools for deciphering RCS-dependent biology but also a general design platform for developing ABS probes for a broader range of biological analytes encompassing elements across the periodic table.}, journal={Accounts of Chemical Research}, year={2019}, month={Sep} }
 @article{ohata_krishnamoorthy_gonzalez_xiao_iovan_toste_miller_chang_2019, title={An Activity-Based Methionine Bioconjugation Approach to Developing Proximity-Activated Imaging Reporters}, volume={10}, url={https://doi.org/10.26434/chemrxiv.9964256.v1}, DOI={10.26434/chemrxiv.9964256.v1}, abstractNote={Chemical probes that report on protein activity, rather than protein abundance, with spatial and temporal resolution can enable studies of their native function in biological contexts as well as provide opportunities for developing new types of biochemical reporters. Here we present a sensing platform, termed proximity-activated imaging reporter (PAIR), which combines activity-based methionine bioconjugation and antibody labeling with proximity-dependent oligonucleotide-based amplification to monitor dynamic changes of a given analyte in cells and animals through context-dependent methionine labeling of specific protein targets. We establish this PAIR method to develop sensors for imaging reactive oxygen species (ROS) and calcium ions through oxaziridine-directed labeling of reactive methionine residues on β-actin and calmodulin (CaM), respectively, where the extent of methionine bioconjugation on these protein targets can serve as an indicator of oxidative stress or calcium status. In particular, application of PAIR to activity-based CaM detection provides a method for imaging integrated calcium activity in both in vitro cell and in vivo zebrafish models. By relying on native protein biochemistry, PAIR enables redox and metal imaging without introduction of external small-molecules or genetically encoded indicators that can potentially buffer the natural/existing pools. This approach can be potentially generalized to target a broader range of analytes by pairing appropriate activity-based protein probes with protein detection reagents in a proximity-driven manner, providing a starting point not only for designing new sensors but also for monitoring endogenous activity of specific protein targets in biological specimens with spatial and temporal fidelity.}, publisher={American Chemical Society (ACS)}, author={Ohata, Jun and Krishnamoorthy, Lakshmi and Gonzalez, Monica and Xiao, Tong and Iovan, Diana and Toste, F. Dean and Miller, Evan and Chang, Christopher}, year={2019}, month={Oct} }
 @article{ohata_martin_ball_2019, title={Metallvermittelte Funktionalisierung natürlicher Peptide und Proteine: Biokonjugation mit Übergangsmetallen}, volume={131}, url={https://doi.org/10.1002/ange.201807536}, DOI={10.1002/ange.201807536}, abstractNote={Abstract Die selektive Modifikation natürlicher Proteine stellt eine enorme methodologische Herausforderung dar und bedarf einer strikten Kontrolle der Selektivität und des Umfangs einer Reaktion. Demnach existiert ein fortwährender Bedarf an neuen Reaktivitäts‐ sowie Selektivitätskonzepten. Übergangsmetalle zeichnen sich durch ihre Fülle einzigartiger Reaktivitäten aus, welche biologischen Reaktionen und Prozessen gegenüber orthogonal sind. Folglich spielen metallbasierte Methoden eine zunehmend wichtige Rolle in der Biokonjugationschemie. In diesem Aufsatz werden metallbasierte Methoden sowie deren Reaktivitäten und Selektivitäten bei der Funktionalisierung natürlicher Proteine und Peptide diskutiert.}, number={19}, journal={Angewandte Chemie}, publisher={Wiley}, author={Ohata, Jun and Martin, Samuel C. and Ball, Zachary T.}, year={2019}, month={May}, pages={6238–6264} }
 @article{ohata_martin_ball_2019, title={Metal‐Mediated Functionalization of Natural Peptides and Proteins: Panning for Bioconjugation Gold}, volume={58}, url={https://doi.org/10.1002/anie.201807536}, DOI={10.1002/anie.201807536}, abstractNote={Selective modification of natural proteins is a daunting methodological challenge and a stringent test of selectivity and reaction scope. There is a continued need for new reactivity and new selectivity concepts. Transition metals exhibit a wealth of unique reactivity that is orthogonal to biological reactions and processes. As such, metal-based methods play an increasingly important role in bioconjugation. This Review examines metal-based methods as well as their reactivity and selectivity for the functionalization of natural proteins and peptides.}, number={19}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Ohata, Jun and Martin, Samuel C. and Ball, Zachary T.}, year={2019}, month={May}, pages={6176–6199} }
 @article{hanaya_ohata_miller_mangubat-medina_swierczynski_yang_rosenthal_popp_ball_2019, title={Rapid nickel(ii)-promoted cysteine S-arylation with arylboronic acids}, url={https://doi.org/10.1039/C9CC00159J}, DOI={10.1039/C9CC00159J}, abstractNote={S-Arylation of cysteine residues is an increasingly powerful tool for site-specific modification of proteins, providing novel structure and electronic perturbation. The present work demonstrates an operationally-simple cysteine arylation reaction 2-nitro-substituted arylboronic acids, promoted by a simple nickel(ii) salt. The process exhibits strikingly fast reaction rates under physiological conditions in purely aqueous media with excellent selectivity toward cysteine residues. Cysteine arylation of natural proteins and peptides allows attachment of useful reactive handles for stapling, imaging, or further conjugation.}, journal={Chemical Communications}, publisher={Royal Society of Chemistry (RSC)}, author={Hanaya, Kengo and Ohata, Jun and Miller, Mary K. and Mangubat-Medina, Alicia E. and Swierczynski, Michael J. and Yang, David C. and Rosenthal, Reece M. and Popp, Brian V. and Ball, Zachary T.}, year={2019} }
 @article{ohata_zeng_segatori_ball_2018, title={A Naturally Encoded Dipeptide Handle for Bioorthogonal Chan-Lam Coupling}, volume={57}, DOI={10.1002/anie.201800828}, abstractNote={Manipulation of biomacromolecules is ideally achieved through unique and bioorthogonal chemical reactions of genetically encoded, naturally occurring functional groups. The toolkit of methods for site-specific conjugation is limited by selectivity concerns and a dearth of naturally occurring functional groups with orthogonal reactivity. We report that pyroglutamate amide N-H bonds exhibit bioorthogonal copper-catalyzed Chan-Lam coupling at pyroglutamate-histidine dipeptide sequences. The pyroglutamate residue is readily incorporated into proteins of interest by natural enzymatic pathways, allowing specific bioconjugation at a minimalist dipeptide tag.}, number={15}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Ohata, Jun and Zeng, Yimeng and Segatori, Laura and Ball, Zachary T.}, year={2018}, month={Mar}, pages={4015–4019} }
 @article{ohata_miller_mountain_vohidov_ball_2018, title={A Three-Component Organometallic Tyrosine Bioconjugation}, volume={57}, DOI={10.1002/anie.201711868}, abstractNote={Metal-based bioconjugation linkages represent a little-studied approach to protein functionalization that provides novel reactivity, stability, and function. Described is an organometallic bioconjugation, employing rhodium(III) salts, to link boronic acids with tyrosine residues by an arene complex. Both peptides and proteins are amenable to the mild bioconjugation in aqueous media, allowing incorporation of useful functionalities, such as affinity handles or fluorophores. Because of the metastability of the inorganic linkage, the conjugates are susceptible to cleavage by nucleophilic redox mediators but are stable toward typical biological conditions.}, number={11}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Ohata, Jun and Miller, Mary K. and Mountain, Courtney M. and Vohidov, Farrukh and Ball, Zachary T.}, year={2018}, month={Feb}, pages={2827–2830} }
 @article{ohata_ball_2018, title={Rhodium at the Chemistry-Biology Interface}, url={https://doi.org/10.1039/C8DT03032D}, DOI={10.1039/c8dt03032d}, abstractNote={As a rare element with no known natural biological function, rhodium has a limited history in biological chemistry and chemical biology. However, rhodium complexes have unique structure and reactivity attributes, and chemists have increasingly used these attributes to probe and perturb living systems. This brief review focuses on recent advances in the use of rhodium complexes in biological contexts, including medicinal chemistry, protein science, and chemical biology. In particular, we highlight both structure- and reactivity-driven approaches to biological probes and discuss how coordination environment affects molecular properties in a biological environment.}, journal={Dalton Transactions}, publisher={Royal Society of Chemistry (RSC)}, author={Ohata, Jun and Ball, Zachary Thomas}, year={2018} }
 @article{ohata_ball_2017, title={A Hexa-rhodium Metallopeptide Catalyst for Site-Specific Functionalization of Natural Antibodies}, volume={139}, DOI={10.1021/jacs.7b06428}, abstractNote={Preparation of antibody-drug conjugates (ADCs), an emerging novel class of highly targeted biological hybrid agents, necessitates precise control of conjugation reactivity. Antibodies have complex multistranded architectures, and specific modification of natural antibodies has proven quite challenging. Here, we demonstrate that cooperative activity of a multimetallic metallopeptide enables efficient site-specific antibody functionalization, based on molecular recognition of the constant Fc region. This interplay of multiple metal centers enables introduction of an orthogonal alkyne handle into monoclonal or polyclonal antibodies from different species in an Fc-specific fashion. Elaboration of this simple functionalization allows preparation of conjugates with fluorophore, affinity handle, and pharmacological agents. This method opens a new opportunity for quick and easy production of well-defined antibody conjugates from a variety of antibody sequence and species of origin.}, number={36}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Ohata, Jun and Ball, Zachary T.}, year={2017}, month={Aug}, pages={12617–12622} }
 @article{ohata_ball_2017, title={Ascorbate as a pro-oxidant: mild N-terminal modification with vinylboronic acids}, volume={53}, DOI={10.1039/c6cc09955f}, abstractNote={We describe divergent reactivity of vinylboronic acids for protein modification. In addition to previously reported copper-catalyzed backbone N-H modification, ascorbate in air mediates N-terminal functionalization with the same vinylboronate reagents. This mild and selective aqueous reactivity enables selective single-modification of the B chain of human insulin.}, number={10}, journal={Chemical Communications}, publisher={Royal Society of Chemistry (RSC)}, author={Ohata, Jun and Ball, Zachary T.}, year={2017}, pages={1622–1625} }
 @article{ohata_minus_abernathy_ball_2016, title={Histidine-Directed Arylation/Alkenylation of Backbone N–H Bonds Mediated by Copper(II)}, volume={138}, DOI={10.1021/jacs.6b03390}, abstractNote={Chemical modification of proteins and peptides represents a challenge of reaction design as well as an important biological tool. In contrast to side-chain modification, synthetic methods to alter backbone structure are extremely limited. In this communication, copper-mediated backbone N-alkenylation or N-arylation of peptides and proteins by direct modification of natural sequences is described. Histidine residues direct oxidative coupling of boronic acids at the backbone NH of a neighboring amino acid. The mild reaction conditions in common physiological buffers, at ambient temperature, are compatible with proteins and biological systems. This simple reaction demonstrates the potential for directed reactions in complex systems to allow modification of N-H bonds that directly affect polypeptide structure, stability, and function.}, number={24}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Ohata, Jun and Minus, Matthew B. and Abernathy, Morgan E. and Ball, Zachary T.}, year={2016}, month={Jun}, pages={7472–7475} }
 @article{ohata_vohidov_ball_2015, title={Convenient analysis of protein modification by chemical blotting with fluorogenic “click” reagents}, volume={11}, DOI={10.1039/c5mb00510h}, abstractNote={Direct visualization of bioorthogonal alkyne or azide handles using fluorogenic azide-alkyne cycloaddition conducted on the surface of a blot membrane. The method eliminates the need for separation steps to remove excess small molecule reagents before attachment of antigen molecules or other visualization handles, and is especially useful for the analysis of peptides and small proteins. A variety of potential fluorogenic reagents are assessed, and sensitivity (<0.1 picomole) similar to current commercially available fluorescence imaging methods is possible.}, number={11}, journal={Molecular BioSystems}, publisher={Royal Society of Chemistry (RSC)}, author={Ohata, Jun and Vohidov, Farrukh and Ball, Zachary T.}, year={2015}, pages={2846–2849} }
 @article{ohata_vohidov_aliyan_huang_martí_ball_2015, title={Luminogenic iridium azide complexes}, volume={51}, DOI={10.1039/c5cc06099k}, abstractNote={The synthesis and characterization of luminogenic, bioorthogonal iridium probes is described. These probes exhibit long photoluminescence lifetimes amenable to time-resolved applications. A simple, modular synthesis via 5-azidophenanthroline allows structural variation and allows optimization of cell labeling.}, number={82}, journal={Chemical Communications}, publisher={Royal Society of Chemistry (RSC)}, author={Ohata, Jun and Vohidov, Farrukh and Aliyan, Amirhossein and Huang, Kewei and Martí, Angel A. and Ball, Zachary T.}, year={2015}, pages={15192–15195} }
 @article{vohidov_knudsen_leonard_ohata_wheadon_popp_ladbury_ball_2015, title={Potent and selective inhibition of SH3 domains with dirhodium metalloinhibitors}, volume={6}, DOI={10.1039/c5sc01602a}, abstractNote={Specific, designed histidine–rhodium interactions allow a metallopeptide to bind Lyn kinase with nanomolar affinity and to activate kinase activity.}, number={8}, journal={Chemical Science}, publisher={Royal Society of Chemistry (RSC)}, author={Vohidov, Farrukh and Knudsen, Sarah E. and Leonard, Paul G. and Ohata, Jun and Wheadon, Michael J. and Popp, Brian V. and Ladbury, John E. and Ball, Zachary T.}, year={2015}, pages={4778–4783} }
 @article{takemoto_ohata_umetani_yamaguchi_matsuzaka_2014, title={A Diruthenium μ-Carbido Complex That Shows Singlet-Carbene-like Reactivity}, volume={136}, DOI={10.1021/ja509364d}, abstractNote={Low-temperature deprotonation of the cationic μ-methylidyne complex [(Cp*Ru)2(μ-NPh)(μ-CH)][BF4] (Cp* = η5-C5Me5) with KN(SiMe3)2 affords a thermally unstable μ-carbido complex [(Cp*Ru)2(μ-NPh)(μ-C)] (2), as evidenced by trapping experiments with elemental S or Se and 13C NMR spectroscopic observation. The reactivity of 2 toward CO2, Ph2S+CH2–, EtOH, and an intramolecular C–H bond indicates that the μ-carbido carbon in 2 has an ambiphilic (nucleophilic and electrophilic) nature consistent with the formulation of 2 as the first example of a transition-metal-substituted singlet carbene. DFT study suggests that the Ru substituents in 2 are stronger σ-donor and weaker π-donor to the carbene center than amino substituents in N-heterocyclic carbenes.}, number={45}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Takemoto, Shin and Ohata, Jun and Umetani, Kento and Yamaguchi, Masahiro and Matsuzaka, Hiroyuki}, year={2014}, month={Nov}, pages={15889–15892} }